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- PDB-1nvo: Solution structure of a four-helix bundle model, apo-DF1 -

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Basic information

Entry
Database: PDB / ID: 1nvo
TitleSolution structure of a four-helix bundle model, apo-DF1
ComponentsHomodimeric Alpha2 Four-Helix Bundle
KeywordsUNKNOWN FUNCTION / De Novo Protein Design / Alpha-Helical Bundle / Diiron Protein Model
Function / homologyImmunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Function and homology information
MethodSOLUTION NMR / Torsion Angle Dynamics, Simulated Annealing, Energy Restrained Minimization
AuthorsMaglio, O. / Nastri, F. / Pavone, V. / Lombardi, A. / DeGrado, W.F.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Preorganization of molecular binding sites in designed diiron proteins
Authors: Maglio, O. / Nastri, F. / Pavone, V. / Lombardi, A. / DeGrado, W.F.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Retrostructural Analysis of Metalloproteins. Application to the Design of a Minimal Model for Diiron Proteins
Authors: Lombardi, A. / Summa, C.M. / Geremia, S. / Randaccio, L. / Pavone, V. / DeGrado, W.F.
#2: Journal: CURR.OPIN.STRUCT.BIOL. / Year: 1999
Title: Tertiary Templates for the Design of Diiron Protein
Authors: Summa, C.M. / Lombardi, A. / Lewis, M. / DeGrado, W.F.
#3: Journal: J.Am.Chem.Soc. / Year: 2001
Title: Toward the De Novo Design of a Catalytically Active Helix Bundle: a Substrate-Accessible Carboxylate-Bridged Dinuclear Metal Center
Authors: Di Costanzo, L. / Wade, H. / Geremia, S. / Randaccio, L. / Pavone, V. / DeGrado, W.F. / Lombardi, A.
#4: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2003
Title: Sliding Helix and Change of Coordination Geometry in a Model di-Mn(II) Protein
Authors: DeGrado, W.F. / Di Costanzo, L. / Geremia, S. / Lombardi, A. / Pavone, V. / Randaccio, L.
History
DepositionFeb 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homodimeric Alpha2 Four-Helix Bundle
B: Homodimeric Alpha2 Four-Helix Bundle


Theoretical massNumber of molelcules
Total (without water)11,7422
Polymers11,7422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 40structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Homodimeric Alpha2 Four-Helix Bundle


Mass: 5870.894 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically Synthesized
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 1.0 mM protein concentration; 90% H2O, 10% DMSO / Solvent system: 90% H2O, 10% DMSO
Sample conditionspH: 4 / Pressure: Ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio et al.processing
DYANA1.5Guentert et al.structure solution
Amber7Case et al.refinement
RefinementMethod: Torsion Angle Dynamics, Simulated Annealing, Energy Restrained Minimization
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 14

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